In Issue 36, James (one of the main characters) is "PENCIL'D!" after having a rant. Likewise, Mr. Rodwell (a teacher) is "MR. T'D!" in Issue 51. The character Megaba is also created when several Mokuba clones are "FUSE'D!" in Issue 98.

In the August 22, 2003 strip, a character in the likeness of Homestar named "Mr. Runner" suggests a ridiculous ad campaign with muffins and toast to a car insurance company and is promptly "shown the window".

In the September 10, 2003 strip, Homestar pops out of the characters pants and says "A jorb well done".

In the April 3, 2004 strip, Strong Bad's head is shown, with nearby text saying "oh noe its stwong bah!"

Issue 1 of Dragon Master's comics features DM checking his email while singing to himself like Strong Bad.
In Issue 17, Label Buddy (the idiot who is killed quite often) is kicked in the face with the caption "KICKEDED!" in the following panel.
In Issue 33, Label Buddy chokes on a speck of dirt and gets "HEIMLICH MANEUVER'D!"
In Issue 34, he is "SHOTGUNNED!"
Label Buddy faints with the caption, "FAINTED!" and is run over Halo style with the caption "SPLATTERED!" in Issue 40
Lekonua the intelligent robot gets "SHURIKENED!" in Issue 42.This Comic of Leko's is titled "Hit Strong Bad First" and the Brothers Chaps are number one on the hit list.
One of the advertisement banners shows Label Buddy asking for his lines like Homestar does in First Time Here?
In Episode 20 of Leko's Sprite Comic, one of the "dramatic questions" asks how Strong Bad types with boxing gloves, and Human Leko mentions the HR Wiki just after it.

Comic #40 on Week 6 has a reference from the Strong Bad Emailfingers. The character, Hardhat is wearing the same arms as Homestar Runner wears in the said email. There's even a link to the email at the bottom of the comic for those who have never heard of Homestar Runner.

Issue #4 - sonicstarrunner.com. Sonic the Hedgehog characters on a Homestar Runner Main Page, which also makes a joke out of rapidly flicking the cursor over the buttons, causing multiple effects to occur on the screen. sonicstarrunner.com is a page with search links and no website.

The author of "Evil Inc" has said on the Bob and George forums that Satan being dressed up as Ichiro in comic #267 is a minor reference to Strong Bad dressing up as Homestar dressed up as Angus Young in Pumpkin Carve-nival.

On this blog post, depicting of what appears to be a PhotoShopped Life cereal box, Scott says "Thanks to Darrel for the great jorb!"

gamerman, not recognizing the reference, asked if "you meant job", though kokoman points out the site, Scott replied: "gamerman: That depends on whether or not you have ever seen Strong Bad before, and know who Coach Z is."

The artist, Scott DeWitt, is a Homestar Runner fan. One of the main characters, Lemmy, has it on his iPod, Sylvia's friend Kirstin has Strong Bad on her bag, and there was a reference to Teen Girl Squad in his drawing tutorial prior to the tutorial's removal. Also, after F@NBOY$ won the Joystiq Wrap-up, and the cast thinks they're internet celebrities, Strong Bad is among those laughing at them.

A comic called The Homestarmy was made after it was found out about the wiki and his entry in the sightings. Strong Bad then instructs The Cheat to take out Lemmy with a sniper rifle.

Types (now in stereo). Paul is thinking of more ideas for the comic. He gives up and throws away the notepad. All it has on it are pictures of So and So, Cheerleader, The Ugly One and What's Her Face, respectively.

In the comic called First Day on the Job Part 8 When the Xbox falls on Lemmy's head the boxes next to it are for Rhino Feeder and "Secret Collect 2", both have pictures of Strong Bad on the cover. There is also what appears to be a Homestar Runner keychain or pez dispenser in the last panel.

In the comic Popular Trends, in the final panel, which has a Muppet Babies parody, the blocks on the floor spell H*R, the abbreviation for Homestar Runner.

In Piece de Resistance, Paul is playing online and as he kills his enemies, they drop out of the game and one of them is named So and so.

The old F@nboy$ Mini #12 (no longer available) starts off with a description of Mario as such: He's short, dumpy, chubby, silly-looking and always has a smile on his face. He is an OK guy." The last sentence is a reference to flashback.

Cash'd was used again in Shady Deals when Paul bribes the grim reaper.

The first panel of the old F@nb0y$ Mini #20 has Homestar's face on the microphone.

On December 10, 2007, when Scott Dewitt posted a comic about his writer's block, an updated blog post was put up and the previous one (which was basically everything stated in the comic that day) was replaced with "Baleeted"

The image file name for one of the smilies on his forum, "Krudsome," (his name on the forums and his email address is "Krudman") is "Mah_face," a reference to the chair.

In the fourth comic, "Obligatory Pop Culture Reference," Dangeresque Too makes a small cameo on the last panel.
The fifth comic's title, "Burninated", is an obvious reference to Trogdor.
The seventh comic's title, "Got Witch's Brew?" is a reference to Homestar's obsession with witch's brew.

In the December 2003 issue of DC Comic's Hawkman (page 16 of issue 20, volume 4), an abusive spouse is seen wearing a black T-shirt featuring Strong Bad's face and gloves, and the text "FHGWHGAS." Unfortunately you'll have to pick up an old issue of the comic to see it. [7]

In "47- Meet Pointyhead", one of the computers Kerny passes whilst shopping is the shotgunned Compy 386. Kerny remarks that he needs a computer "a little less slightly shotgunned."

In addition, the computer he ends up buying, the PC Plum, seen here, bears particular resemblance to the semi-repaired Tandy 400, with burn marks, tape and cracked screen, not to mention contrast buttons akin to those on the Tandy pre-explosion.

The header joke for the March 31 2007 comic reads "Subject: SB_Email Menu"; the fourth panel of the same comic shows Rayne, the main character, typing on a computer in near-identical fashion to Strong Bad.

On June 28, 2003, in an effort to find what's funny, the comic decided to make a parody of Strong Bad Email with the comic's own characters. The original site is gone, but the comic can be seen through the Web Archive content warning.

A filler comic on how to make your own comic strip suggests drawing copyrighted characters. The Cheat is among them.

During the Death/Hulamutt Action Hour storyline, the Anecdotist had figured the authorities would send the Green Lantern to battle him, and assembled a group of yellow characters to protect him. Among them is The Cheat.

In another, the "Regular Ninja" parodies the Strong Bad Email element, including a "How do you type with boxing gloves"-type question. The animation ends with a single panel, like the normal comic: "Regular Ninja vs. Wrestleman Ninja"

In comic #16, the caption reads, "I am also working on a new and more better (more...more better...hehe Strongbad) site design," referring to the interview email.

In comic #265, while Faye and Marten are discussing what will be the next indie rock band to break up, Faye mentions that the head of Win Butler (from The Arcade Fire) will explode during a live performance, forcing them to replace him with a Homestar Runner puppet.

The first two lines of the 16th comic are "So from then on, it was all pork and beans." and "That's not very healthy..." which are close to the two lines of dialogue said by Homestar and Marzipan in helium.

In the July 23, 2003 comic, when Moses is altering how he percieves the afterlife, one of his visualisations bears a resemblance to Strong Bad standing in Strong Badia, saying 'Pop culture reference!'.

In the July 2005 issue of this Marvel Comics publication, as the title characters head off on a mission to rescue the captive mother of their newest accquaintance, Victor, Victor himself remarks that he is "not sure why he should entrust his mom's life to the freakin' Teen Girl Squad!" Chase, the only male member of the Runaways team, corrects him with: "That's Teen Girl Squad plus one, amigo!"

The weekly filler Meanwhile in the Dimension of Pain shows the demons deathmatching. When Horribus uses the Unholy Hand grenade and the demons are all incinerated, the panel reads "And all was laid to burnination."
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The Top Ten spin-off comic SMAX puts Jaafs Macksun and his partner Toybox in a world of fantasy. In Issue, #2, the design on the back of Toybox's jacket turns into the faces of Homestar and Strong Bad. In issue #3, a wanted poster for Trogdor is on a pole and the silhouette of Homestar and Pom Pom are seen in town.

In comic 187, a hyperactive, bomb-wielding character called Bean shouts, "Get clear! Get clear! I'll a'splode him good!" As a reference to Vector Strong Bad.
In sub-series comic Sonic Universe issue 23, the same character quotes Homestar's line about times from the sbemail animal.

In the online webcomic, Staccato, when the author portrays his characters as Fantastic Four characters, the one portrayed as the "The Human Torch" says "'The Human Torch?' 'Flame On?' That all sounds kinda' fruity... Couldn't I be be called like 'The Burninator' or something?" in direct reference to Trogdor.
[10]

In issue #44, Superman and Batman spy on a grossly inaccurate movie production of their origins. The actor playing Batman declares, in a line of dialogue for the film, that he and Superman should visit their headquarters "on the moooooooon!"

In Comic 100, click on "100 Comics" at the end to see Pantsman answer an email on the Compy 386. Strong Bad later appears and repeats a line from sibbie in this clip.

In the 6th panel of Comic 135, a The Cheat Talking Plush Doll is visible with the rest of the merchandise behind the glass in the bottom right.

At the top of the new layout, there is a rotating image, featuring several different quotes. A few of them are [How do you type with boxing gloves on?], [We are the band LIMOZEEN!] and [Let's get ready to look SO GOOD!]

The title for the news post on Saturday, September 10, 2005 at 12:43 PM is "Throw baby", a Peasant's Quest reference.

The origin of the Witch's Brew name came from Homestar's famous Halloween witch's brew line. (Alas, however, the phrase is not spelled correctly in the comic.) Also, in the first comic, Homestar appears on the last panel, and the third comic uses the CHILDREN! panel from Teen Girl Squad. The sixth comic tells us to not fake the funk on a nasty dunk, one of Homsar's quotes from interview. And the author bios describe one of the creators as "one of the few lucky non-peasant humans to be burninated."

Also in the bonus section, there is a thing called "Flame War 04." The first comic is a reference to the Strong Bad Email dragon, and the state (California) with the underwear is a reference to Strong Bad Email weird dream.